Building your own is definitely the way to go if you're looking for power. There isn't really much you can screw up, either, unless you drop it or spill Coke all over everything. Many of the computer parts stores around here absolutely insist that THEY be the ones to install the RAM and plug in the CPU, and they do it for free.
Those were the only two things that you could really break something with, and the new CPU fans are notoriously fiendish.
As for all the other parts, the main rule when building a computer nowadays is "if it doesn't fit, it doesn't go there."